ExFiT: Ensemble-based Excited-State Character Fingerprinting across Temperatures

Repository Description This repository contains all data, computational outputs, and analysis scripts used for the ExFiT study: Ensemble-based Excited-State Character Fingerprinting across Temperatures. It provides equilibrium geometries, finite-temperature Wigner ensembles, quantum-chemical outputs, excited-state descriptor data, and post-processing scripts used to characterize the temperature-dependent excited-state behavior of four representative chromophores: trans-Azobenzene, (E)-Hemithioindigo (HTI), para-Nitroaniline (PNA), and Coumarin 481 (C481).The archive is organized into four top-level folders to ensure full transparency of the computational workflow: 1. TeraChem Contains all static (equilibrium-geometry) quantum-chemical outputs, computed at the CAM-B3LYP-D3/Ahlrichs-pVDZ level using TeraChem. terachem.out — Output files for equilibrium-geometry vertical excitation (absorption) and harmonic frequency (IR) calculations, for all four molecules. Dipole moments — Ground-state, excited-state (relaxed and unrelaxed), and transition dipole moments for all systems. Raw IR data — Harmonic vibrational frequencies and IR intensities at the optimized ground-state geometry. Raw absorption data — Vertical excitation energies and oscillator strengths, provided both in eV and nm. Broadened absorption spectra — Gaussian-broadened absorption profiles (FWHM = 0.7 eV), in nm, for all four molecules. Charge density difference (CDD) figures — Excitation-resolved CDD isosurface images for the first 20 singlet excited states of all four molecules, illustrating electron accumulation (blue)/depletion (orange) patterns upon excitation. 2. NewtonX Contains the finite-temperature Wigner sampling inputs and outputs generated with Newton-X, used to build the nuclear ensembles for each molecule at 200, 300, and 400 K. Equilibrium geometry files — .xyz and .molden files for each molecule's optimized ground-state structure and normal modes, used as the reference structure and frequency input for Wigner sampling. initqp.input — Newton-X input files for Wigner ensemble generation, provided separately for each of the three temperatures (200 K, 300 K, 400 K) and each molecule. Cross-section data — Simulated nuclear-ensemble absorption cross-section data points (temperature-broadened spectra) for all three temperatures, for all four molecules. 3. TheoDORE Contains the complete excited-state descriptor analysis for every sampled geometry across the Wigner ensembles, computed with the TheoDORE package. Data is organized as compressed archives, one per molecule per temperature, each containing 501 subfolders (geom_001 – geom_501) corresponding to the individual ensemble geometries. Each geom_### subfolder contains: dens_ana.in — TheoDORE input file specifying fragment definitions and requested descriptors for that geometry. terachem.out — TeraChem vertical excitation output for that specific ensemble geometry, used as input for the TheoDORE analysis. [molecule].molden — Molden-format file for that ensemble geometry, used for orbital/NTO visualization. nto_A*.mld — Molden files of the natural transition orbitals (NTOs) for each computed excited state. nto_jmol.spt — Jmol script file for rendering the NTO isosurfaces. tden_summ.txt — Summary table of all computed transition-density-matrix descriptors (CT, RMSeh, SHE, PRNTO, COH, PR, etc.) for each excited state at this geometry (the primary per-geometry descriptor output). OmFrag.txt — Fragment-pair-resolved decomposition of the CT number, showing the contribution of each donor/bridge/acceptor fragment pair to the overall charge-transfer character. ehFrag.txt — Fragment-resolved electron and hole population analysis, quantifying how the electron and hole densities are distributed across the defined molecular fragments. theodore.log — Full log file of the TheoDORE run for this geometry. 4. Scripts_&_CSVs Contains the aggregated descriptor datasets and the Python scripts used to generate the figures reported in the main text and Supporting Information. Dataset: Azobenzene_descriptors_all_temps.csv Coumarin_c12_descriptors_all_temps.csv HTI_descriptors_all_temps.csv PNA_descriptors_all_temps.csv Each file aggregates the full per-geometry, per-state TheoDORE descriptor output (extracted from tden_summ.txt across all 501 geometries and all three temperatures) for that molecule into a single tabular dataset, used for all downstream statistical analysis (ensemble averages, standard deviations, PCA, violin plots, state-reordering statistics). PNA_S3_merged_dihedrals_CT.csv: Per-geometry dataset combining the S3 charge-transfer number with structural descriptors (NO2 and NH2 torsional/out-of-plane deviations) for the PNA Wigner ensemble, used to relate the broad CT distribution of PNA to its underlying torsional coordinates. Scripts: plot_crossmolecule.py — Uses the four *_descriptors_all_temps.csv files to generate the cross-molecule comparison figures reported in the main text and SI: ensemble-averaged descriptor trends, PCA fingerprints, violin-plot distributions, bright-state reordering statistics, and POS (charge-transfer direction) distributions. plot_PNA_dihedrals.py — Uses PNA_S3_merged_dihedrals_CT.csv to generate the torsional-distribution plots and the correlation analysis between the CT number and NO₂/NH₂ geometric deviations, supporting the structural interpretation of PNA's broad CT distribution discussed in Section 3.3. Scientific Scope This repository enables detailed reproduction and further analysis of: Temperature-dependent distributions of excited-state descriptors (CT number, electron-hole separation, entanglement entropy, NTO participation ratio) across finite-temperature Wigner ensembles PCA-based excited-state character fingerprints and their temperature dependence Bright-state identity and reordering statistics across thermally sampled geometries Structural (torsional) origins of descriptor variability Nuclear-ensemble-averaged absorption spectra at multiple temperatures Reproducibility All results reported in the manuscript and SI can be reproduced from the data and scripts provided: Equilibrium geometries, normal modes, and Wigner ensemble inputs are included for all four molecules Full per-geometry TDDFT and TheoDORE outputs are provided for all 501 × 3 (temperature) × 4 (molecule) ensemble calculations Descriptor datasets and all plotting scripts used to generate the figures in the manuscript are included